Abstract 5185: Intratumoral <i>Escherichia</i> is associated with response to single-agent immune checkpoint inhibition in patients with advanced non-small cell lung cancer
Authors: Arielle Elkrief, Anita S. Bowman, Ayyuce Begum Bektas, Wenfei Kang, Katia Manova-Todorova, Jacklynn V. Egger, Hira Rizvi, Daniel Kelly, Eric Chan, Eric Rosiek, Fan Ning, Gregory J. Riely, Álvaro Quintanal Villalonga, Snjezana Dogan, Umesh Bhanot, Mithat Gonen, Matthew D. Hellmann, Adam J. Schoenfeld, Charles M. Rudin, Marc Ladanyi, Chad M. Vanderbilt
Journal: Cancer Research (2023)

Abstract The impact of the intratumoral microbiome on immune checkpoint inhibitor (ICI) efficacy in patients (pts) with non-small cell lung cancer (NSCLC) is unknown. In preclinical studies, the presence of lung intratumoral Escherichia was associated with a proinflammatory tumor microenvironment and decreased metastases within lung tissue. We sought to detect intratumoral bacteria in pts with advanced NSCLC using hybrid capture-based, next generation sequencing (NGS). We studied 849 pts treated with ICI-based therapy who underwent NGS at our center. We extracted unmapped reads from BAM files, and these were queried for bacteria (blastn alignment using the NCBI database). Putative environmental contaminants were subtracted from the analysis using “no template” controls (n=2,539) to exclude possible artifactual false positives. A custom E.Coli fluorescence in situ hybridization (FISH) probe was used to visualize Escherichia within the tumors after co-registration with H&amp;E. In 849 pts, a median of 30 bacterial reads was detected per sample (inter-quartile range (18-85)). Among 68 pts with paired primary/metastatic samples, the bacterial spectra were similar in both sites, suggesting that tumor resident bacteria might travel with cancer cells to distant sites. Antibiotic use within 30 days of tumor sampling was associated with decreased intratumoral bacterial diversity (p=0.023 by Inverse Simpson, p=0.038 by Shannon). Intratumoral Escherichia was associated with better PFS (HR 0.78, 95% CI 0.62-0.98, p=0.036), and OS (HR 0.74, 95% CI 0.58-0.95, p=0.017) in pts treated with single-agent ICI, but not combination Chemo/ICI. In a multivariable model adjusting for prognostic features in NSCLC including PD-L1 tumor proportion score, the presence of intratumoral Escherichia was associated with better PFS (p=0.040) and OS (p=0.045) upon single-agent ICI therapy. Escherichia appeared to be intracellular based on co-registration of FISH staining and serial H&amp;E sections. These findings warrant further investigation of the possible inter-relationships between intratumoral Escherichia, tumor immune micro-environment, and ICI therapeutic outcomes. Citation Format: Arielle Elkrief, Anita S. Bowman, Ayyuce Begum Bektas, Wenfei Kang, Katia Manova-Todorova, Jacklynn V. Egger, Hira Rizvi, Daniel Kelly, Eric Chan, Eric Rosiek, Fan Ning, Gregory J. Riely, Álvaro Quintanal Villalonga, Snjezana Dogan, Umesh Bhanot, Mithat Gonen, Matthew D. Hellmann, Adam J. Schoenfeld, Charles M. Rudin, Marc Ladanyi, Chad M. Vanderbilt. Intratumoral Escherichia is associated with response to single-agent immune checkpoint inhibition in patients with advanced non-small cell lung cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5185.